oracle version: 12.2.0.1
As you know, these are then unix processes for the parallel servers in oracle:
ora_p000_ora12c
ora_p001_ora12c
....
ora_p???_ora12c
They can be seen also with the view: gv$px_process.
The spid for each parallel server can be obtained from there.
Then I look for the open files associated with te parallel server here:
ls -l /proc/<spid>/fd
And I'm obtaining around 500-10000 file descriptors for several parallel servers equal to this one:
991 -> /u01/app/oracle/admin/ora12c/dpdump/676185682F2D4EA0E0530100007FFF5E/ORA_DUMMY_FILE.f (deleted)
I've deleted them using:(actually I've create a small script for doing it because there are thousands of them)
gdb -p <spid>
gdb> p close(<fd_id>)
But after some hours the file descriptors start being created again (hundreds every day)
If they are not deleted then eventually the linux limit is reached and any parallel query throws an error like this:
ORA-12801: error signaled in parallel query server P001
ORA-01116: error in opening database file 132
ORA-01110: data file 132: '/u02/oradata/ora12c/pdbname/tablespacenaname_ts_1.dbf'
ORA-27077: too many files open
Does anyone have any idea of how and why this file descriptors are being created, and how to avoid it?.
Edited: Added some more information that could be useful.
I've tested that when a new PDB is created a directory DATA_PUMP_DIR is created in it (select * from all_directories) that is pointing to:
/u01/app/oracle/admin/ora12c/dpdump/<xxxxxxxxxxxxx>
The linux directory is also created.
Also one file descriptor is created pointing to ORA_DUMMY_FILE.f in the new dpdump subdirectory like the ones described initially
lsof | grep "ORA_DUMMY_FILE.f (deleted)"
/u01/app/oracle/admin/ora12c/dpdump/<xxxxxxxxxxxxx>/ORA_DUMMY_FILE.f (deleted)
This may be ok, the problem I face is the continuos growing of the file descriptors pointing to ORA_DUMMY_FILE that reach the linux limits.
Related
When importing a file into Greenplum,one lines fails,and the whole file is not imported successfully.Is there a way can skip the wrong line and import other data into Greenplum successfully?
Here are my SQL execution and error messages:
copy cjh_test from '/gp_wkspace/outputs/base_tables/error_data_test.csv' using delimiters ',';
ERROR: invalid input syntax for integer: "FE00F760B39BD3756BCFF30000000600"
CONTEXT: COPY cjh_test, line 81, column local_city: "FE00F760B39BD3756BCFF30000000600"
Greenplum has an extension to the COPY command that lets you log errors and set up a certain amount of errors that can occur that won't stop the load. Here is an example from the documentation for the COPY command:
COPY sales FROM '/home/usr1/sql/sales_data' LOG ERRORS
SEGMENT REJECT LIMIT 10 ROWS;
That tells COPY that 10 bad rows can be ignored without stopping the load. The reject limit can be # of rows or a percentage of the load file. You can check the full syntax in psql with: \h copy
If you are loading a very large file into Greenplum, I would suggest looking at gpload or gpfdist (which also support the segment reject limit syntax). COPY is single threaded through the master server where gpload/gpfdist load the data in parallel to all segments. COPY will be faster for smaller load files and the others will be faster for millions of rows in a load file(s).
We have bash script (job wrapper) that writes to a file, launches a job, then at job completion it appends to the file information about the job. The wrapper is run on one of several thousand batch nodes, but has only cropped up with several batch machines (I believe RHEL6) accessing one NFS server, and at least one known instance of a different batch job on a different batch node using a different NFS server. In all cases, only one client host is writing to the files in question. Some jobs take hours to run, others take minutes.
In the same time period that this has occurred, there seems to be 10-50 issues out of 100,000+ jobs.
Here is what I believe to effectively be the (distilled) version of the job wrapper:
#!/bin/bash
## cwd is /nfs/path/to/jobwd
## This file is /nfs/path/to/jobwd/job_wrapper
gotEXIT()
{
## end of script, however gotEXIT is called because we trap EXIT
END="EndTime: `date`\nStatus: Ended”
echo -e "${END}" >> job_info
cat job_info | sendmail jobtracker#example.com
}
trap gotEXIT EXIT
function jobSetVar { echo "job.$1: $2" >> job_info; }
export -f jobSetVar
MSG=“${email_metadata}\n${job_metadata}”
echo -e "${MSG}\nStatus: Started" | sendmail jobtracker#example.com
echo -e "${MSG}" > job_info
## At the job’s end, the output from `time` command is the first non-corrupt data in job_info
/usr/bin/time -f "Elapsed: %e\nUser: %U\nSystem: %S" -a -o job_info job_command
## 10-360 minutes later…
RC=$?
echo -e "ExitCode: ${RC}" >> job_info
So I think there are two possibilities:
echo -e "${MSG}" > job_info
This command throws out corrupt data.
/usr/bin/time -f "Elapsed: %e\nUser: %U\nSystem: %S" -a -o job_info job_command
This corrupts the existing data, then outputs it’s data correctly.
However, some job, but not all, call jobSetVar, which doesn't end up being corrupt.
So, I dig into time.c (from GNU time 1.7) to see when the file is open. To summarize, time.c is effectively this:
FILE *outfp;
void main (int argc, char** argv) {
const char **command_line;
RESUSE res;
/* internally, getargs opens “job_info”, so outfp = fopen ("job_info", "a”) */
command_line = getargs (argc, argv);
/* run_command doesn't care about outfp */
run_command (command_line, &res);
/* internally, summarize calls fprintf and putc on outfp FILE pointer */
summarize (outfp, output_format, command_line, &res); /
fflush (outfp);
}
So, time has FILE *outfp (job_info handle) open the entire time of the job. It then writes the summary at the end of the job, and then doesn’t actually appear to close the file (not sure if this is necessary with fflush?) I've no clue if bash also has the file handle open concurrently as well.
EDIT:
A corrupted file will typically end consist of the corrupted part, followed with the non-corrupted part, which may look like this:
The corrupted section, which would occur before the non-corrupted section, is typically largely a bunch of 0x0000, with maybe some cyclic garbage mixed in:
Here's an example hexdump:
40000000 00000000 00000000 00000000
00000000 00000000 C8B450AC 772B0000
01000000 00000000 C8B450AC 772B0000
[ 361 x 0x00]
Then, at the 409th byte, it continues with the non-corrupted section:
Elapsed: 879.07
User: 0.71
System: 31.49
ExitCode: 0
EndTime: Fri Dec 6 15:29:27 PST 2013
Status: Ended
Another file looks like this:
01000000 04000000 805443FC 9D2B0000 E04144FC 9D2B0000 E04144FC 9D2B0000
[96 x 0x00]
[Repeat above 3 times ]
01000000 04000000 805443FC 9D2B0000 E04144FC 9D2B0000 E04144FC 9D2B0000
Followed by the non corrupted section:
Elapsed: 12621.27
User: 12472.32
System: 40.37
ExitCode: 0
EndTime: Thu Nov 14 08:01:14 PST 2013
Status: Ended
There are other files that have much more random corruption sections, but more than a few were cyclical similar to above.
EDIT 2: The first email, sent from the echo -e statement goes through fine. The last email is never sent due to no email metadata from corruption. So MSG isn't corrupted at that point. It's assumed that job_info probably isn't corrupt at that point either, but we haven't been able to verify that yet. This is a production system which hasn't had major code modifications and I have verified through audit that no jobs have been ran concurrently which would touch this file. The problem seems to be somewhat recent (last 2 months), but it's possible it's happened before and slipped through. This error does prevent reporting which means jobs are considered failed, so they are typically resubmitted, but one user in specific has ~9 hour jobs in which this error is particularly frustrating. I wish I could come up with more info or a way of reproducing this at will, but I was hoping somebody has maybe seen a similar problem, especially recently. I don't manage the NFS servers, but I'll try to talk to the admins to see what updates the NFS servers at the time of these issues (RHEL6 I believe) were running.
Well, the emails corresponding to the corrupt job_info files should tell you what was in MSG (which will probably be business as usual). You may want to check how NFS is being run: there's a remote possibility that you are running NFS over UDP without checksums. That could explain some corrupt data. I also hear that UDP/TCP checksums are not strong enough and the data can still end up corrupt -- maybe you are hitting such a problem (I have seen corrupt packets slipping through a network stack at least once before, and I'm quite sure some checksumming was going on). Presumably the MSG goes out as a single packet and there might be something about it that makes checksum conflicts with the garbage you see more likely. Of course it could also be an NFS bug (client or server), a server-side filesystem bug, busted piece of RAM... possibilities are almost endless here (although I see how the fact that it's always MSG that gets corrupted makes some of those quite unlikely). The problem might be related to seeking (which happens during the append). You could also have a bug somewhere else in the system, causing multiple clients to open the same job_info file, making it a jumble.
You can also try using different file for 'time' output and then merge them together with job_info at the end of script. That may help to isolate problem further.
Shell opens 'job_info' file for writing, outputs MSG and then shall close its file descriptor before launching main job. 'time' program opens same file for append as stream and I suspect the seek over NFS is not done correctly which may cause that garbage. Can't explain why, but normally this shall not happen (and is not happening). Such rare occasions may point to some race condition somewhere, can be caused by out of sequence packet delivery (due to network latency spike) or retransmits which causes duplicate data, or a bug somewhere. At first look I would suspect some bug, but that bug may be triggered by some network behavior, e.g. unusually large delay or spike of packet loss.
File access between different processes are serialized by kernel, but for additional safeguard may be worth adding some artificial delays - sleep timers between outputs for example.
Network is not transparent, especially a large one. There can be WAN optimization devices which are known to cause application issues sometimes. CIFS and NFS are good candidates for optimization over WAN with local caching of filesystem operations. Might be worth looking for recent changes with network admins..
Another thing to try, although can be difficult due to rare occurrences is capture of interesting NFS sessions via tcpdump or wireshark. In really tough cases we do simultaneous capturing on both client and server side and then compare the protocol logic to prove that network is or is not working correctly. That's a whole topic in itself, requires thorough preparation and luck but usually a last resort of desperate troubleshooting :)
It turns out this was actually another issue altogether, apparently to do with an out-of-date page being written to disk.
A bug fix was supplied to the linux-nfs implementation:
http://www.spinics.net/lists/linux-nfs/msg41357.html
mysqldump: Error: 'got error 22 from storage engine' when trying to dump
tablespaces
mysqldump: Got error: 23: Out of resources when opening file '.\database\table.MYD' (Errcode: 24) when using LOCK TABLES
i got this error when trying to make a dump in any database that I select , looks like that database is corrupted , is possible repair that ?
You seem to have reached the maximum number of open files. This limit is either MySQL's or the system's.
increase the value for the open_files_limit in your MySQL configuration file (this directive does not exist in a default installation, so you might need to create it in the [mysqld] section)
increase the limit at system level (but I am not sure this applies to Windows)
Here are some reasons for this error:
Type “source path-to-SQL-file“. BUT, you must follow these rules:
Use the full source command, not the . shortcut.
Have no spaces in your path. I copied mine to a root of a drive. Note that spaces in the file name is OK, just not the path.
Do not quote the file name, even if it has spaces. This gave error 22.
Use forward slashes in the path, e.g., C:/path/to/filename.sql. Otherwise you’ll get error 2.
Do not end with a semicolon.
Please check your read write access to the drive where you have stored your mySQL database.
error 22 occurred usually when you have no write access to that drive.
I'm attempting to create a fs within a file.
under linux it's very simple:
create a blank file size 8 gb
dd of=fsFile bs=1 count=0 seek=8G
"format" the drive:
mkfs.ext2 fsFile
works great.
however under cygwin running from /usr/sbin ./mkfs.ext2
has all kinds of weird errors (i assume because of some abstraction)
But with cygwin i get:
mkfs.ext2: Device size reported to be zero. Invalid partition specified, or
partition table wasn't reread after running fdisk, due to
a modified partition being busy and in use. You may need to reboot
to re-read your partition table.
or even worse (if i try to access a file through /cygdrive/...
mkfs.ext2: Bad file descriptor while trying to determine filesystem size
:(
please help,
Thanks
Well it seems that the way to solve it is to not use any path on the file you wish to modify.
doing that seems to have solved it.
also it seems that my 8 gig file does have a file size that's simply to big, it seems like it resets the size var i.e.
$ /usr/sbin/fsck.ext2 -f testFile8GiG
e2fsck 1.41.12 (17-May-2010)
The filesystem size (according to the superblock) is 2097152 blocks
The physical size of the device is 0 blocks
Either the superblock or the partition table is likely to be corrupt!
Abort? no
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Pass 3: Checking directory connectivity
Pass 4: Checking reference counts
Pass 5: Checking group summary information
testFile8GiG: 122/524288 files (61.5% non-contiguous), 253313/2097152 blocks
Thanks anyway
NOTE: This is a complete re-write of this question. I'd previously conflated some ACL issues with the problem I'm hunting, which is probably why there were no answers.
I have a windows service that uses the standard open/close/write routines to write a log file (it reads stuff from a pipe and stuffs it into the log). A new log file is opened each day at midnight. The system is Windows XP Embedded.
The service runs as the Local System service (CreateService with NULL for the user).
When the service initially starts up, it creates a log file and writes to it with no problems. At this point everything is OK, and you can restart the service (or the computer) with no issues.
However, at midnight (when the day changes), the service creates a new log file and writes to it. The funny thing is, this new log file has the 'read only' flag set. That's a problem because if the service (or the computer) restarts, the service can no longer open the file for writing.
Here's the relevant information from the system with the problem having already happened:
Directory of C:\bbbaudit
09/16/2009 12:00 AM <DIR> .
09/16/2009 12:00 AM <DIR> ..
09/16/2009 12:00 AM 437 AU090915.ADX
09/16/2009 12:00 AM 62 AU090916.ADX
attrib c:\bbbaudit\*
A C:\bbbaudit\AU090915.ADX <-- old log file (before midnight)
A R C:\bbbaudit\AU090916.ADX <-- new log file (after midnight)
cacls output:
C:\ BUILTIN\Administrators:(OI)(CI)F
NT AUTHORITY\SYSTEM:(OI)(CI)F
CREATOR OWNER:(OI)(CI)(IO)F
BUILTIN\Users:(OI)(CI)R
BUILTIN\Users:(CI)(special access:)
FILE_APPEND_DATA
BUILTIN\Users:(CI)(IO)(special access:)
FILE_WRITE_DATA
Everyone:R
C:\bbbaudit BUILTIN\Administrators:(OI)(CI)F
NT AUTHORITY\SYSTEM:(OI)(CI)F
CFN3\Administrator:F
CREATOR OWNER:(OI)(CI)(IO)F
Here's the code I use to open/create the log files:
static int open_or_create_file(char *fname, bool &alreadyExists)
{
int fdes;
// try to create new file, fail if it already exists
alreadyExists = false;
fdes = open(fname, O_WRONLY | O_APPEND | O_CREAT | O_EXCL);
if (fdes < 0)
{
// try to open existing, don't create new file
alreadyExists = true;
fdes = open(fname, O_WRONLY | O_APPEND);
}
return fdes;
}
I'm having real trouble figuring out how the file is getting that read-only flag on it. Anyone who can give me a clue or a direction, I'd greatly appreciate it.
Compiler is VC 6 (Yea, I know, it's so far out of date it isn't funny. Until you realize that we're just now upgraded to XPE from NT 3.51).
The Microsoft implementation of open() has an optional third argument 'pmode', which is required to be present when the second argument 'oflag' includes the O_CREAT flag. The pmode argument specifies the file permission settings, which are set when the new file is closed for the first time. Typically you would pass S_IREAD | S_IWRITE for pmode, resulting in an ordinary read/write file.
In your case you have specified O_CREAT but omitted the third argument, so open() has used whatever value happened to be on the stack at the third argument position. The value of S_IWRITE is 0x0080, so if the value in the third argument position happened to have bit 7 clear, it would result in a read-only file. The fact that you got a read-only file only some of the time, is consistent with stack junk being passed as the third argument.
Below is the link for the Visual Studio 2010 documentation for open(). This aspect of the function's behaviour has not changed since VC 6.
http://msdn.microsoft.com/en-us/library/z0kc8e3z.aspx
Well, I have no idea what the underlying problem is with the 'open' APIs in this case. In order to 'fix' the problem, I ended up switching to using the Win32 APIs for file management (CreateFile, WriteFile, CloseHandle).